Flow chart objects

[jason]

docx4j gives you access to everything in the docx (except for mc:AlternateContent/mc:Choice which is pre-filtered) provided it is valid according to the schema.

Can I get flow chart objects information ?

Per above, yes. Exactly how depends on how you have made your flow chart. Unzip your docx and look at its document.xml. What you see is likely to be ugly...

What about comments and bookmarks in the word document?

Sure.

Consider using content controls instead of bookmarks, since bookmarks are point tags, and so not so nice from an XML processing point of view.